I ended up going to see my GP with the knee pain I was experiencing and after being examined he is 99% certain I've got a pulled muscle/tendon that is causing the pain.
He's advised I don't run or do any leg work in the gym for 2 weeks, that runs out a week on Friday so I'll be dropping back and completing W5 again and then, possibly jump back up to W8 but I'll see how I feel on the runs.
I'm still attending the gym, upper body only and using seated variations of exercises where possible so I'm not just sat at home vegetating.
Happy running everyone.